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content/post/2007-06-20-data-handling.markdown

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+---
+author: einar
+categories:
+- Science
+comments: true
+date: "2007-06-20T17:50:39Z"
+header:
+  image_fullwidth: banner_other.jpg
+slug: data-handling
+title: Data handling
+disable_share: true
+wordpress_id: 264
+---
+
+As the people who read my science related posts already know,[ I'm in the middle of doing meta-analysis]({{ site.url }}/2007/05/28/more-meta-analysis-difficulty/). That brought up a problem, so to speak, and it's related to annotations.
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+<!--more-->Probes on microarrays are referenced to genes (to over-simplify): usually these references are made with the latest version of the genome available. As the map of the genome is not static, but it's a moving target, these annotations tend to become obsolete. And that unfortunately leads to problems when you compare experiments made in different time frames.
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+To be precise, the papers I'm using the data from are from 2005 to 2006, but the actual experiments were performed earlier. One uses the annotation data from the Affymetrix HG-U133A chip, which (along with the whole HG-U133 family) [have been proven to be outdated by Dai and coworkers.](http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16284200&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum) The other uses Entrez Gene identifiers, but some IDs are no longer valid or overlap.
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+How can such a situation be solved? For some experiments there's nothing much to do, perhaps reannotate the IDs using an automated system (I believe this is possible), for others (Affy chips) the paper I linked gives a possible (and effective: we've tested it in our group) solution by creating new "meta-probes" that reflect the updated annotations.
+
+In any case, you should be wary of that, should you want to compare different microarray datasets.